Background: Microorganisms are ubiquitous, yet we are only beginning to understand their diversity and population structure. Social amoebae (Dictyostelia) are a diverse group of unicellular eukaryotic microbes that display a unique social behaviour upon starvation in which cells congregate and then some die to help others survive and disperse. The genetic relationships among co-occurring cells have a major influence on the evolution of social traits and recent population genetic analysis found extensive genetic variation and possible cryptic speciation in one dictyostelid species \((Dictyostelium purpureum)\). To further characterize the interplay among genetic variation, species boundaries, social behaviour, and reproductive isolation in the Dictyostelia, we conducted phylogenetic analyses and mating experiments with the geographically widespread social amoeba \(Dictyostelium giganteum\). Results: We sequenced approximately 4,000 basepairs of the nuclear ribosomal DNA from 24 isolates collected from Texas, Michigan, Massachusetts, Virginia, and Wisconsin and identified 16 unique haplotypes. Analyses of the sequence data revealed very little genetic differentiation among isolates and no clear evidence of phylogenetic structure, although there was evidence for some genetic differentiation between the Massachusetts and Texas populations. These results suggest that sexual mating (macrocyst formation) is not likely to correlate with either genetic or geographical distance. To test this prediction, we performed 108 mating experiments and found no association between mating probability and genetic or geographical distance. Conclusions: \(D. giganteum\) isolates from across North America display little genetic variation, phylogeographic structure, and genetic differentiation among populations relative to the cryptic species observed within \(D. purpureum\). Furthermore, variation that does exist does not predict the probability of mating among clones. These results have important implications for our understanding of speciation and social evolution in microbes.